Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F102272011
angle_harmonic.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Tue, Feb 18, 23:39
Size
7 KB
Mime Type
text/x-c
Expires
Thu, Feb 20, 23:39 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
24321272
Attached To
rLAMMPS lammps
angle_harmonic.cpp
View Options
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "angle_harmonic.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
#define SMALL 0.001
/* ----------------------------------------------------------------------
free all arrays
------------------------------------------------------------------------- */
AngleHarmonic::~AngleHarmonic()
{
if (allocated) {
memory->sfree(setflag);
memory->sfree(k);
memory->sfree(theta0);
}
}
/* ---------------------------------------------------------------------- */
void AngleHarmonic::compute(int eflag, int vflag)
{
int i1,i2,i3,n,type,factor;
double delx1,dely1,delz1,delx2,dely2,delz2,rfactor,dtheta,tk;
double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22,vx1,vx2,vy1,vy2,vz1,vz2;
energy = 0.0;
if (vflag) for (n = 0; n < 6; n++) virial[n] = 0.0;
double **x = atom->x;
double **f = atom->f;
int **anglelist = neighbor->anglelist;
int nanglelist = neighbor->nanglelist;
int nlocal = atom->nlocal;
int newton_bond = force->newton_bond;
for (n = 0; n < nanglelist; n++) {
i1 = anglelist[n][0];
i2 = anglelist[n][1];
i3 = anglelist[n][2];
type = anglelist[n][3];
if (newton_bond) factor = 3;
else {
factor = 0;
if (i1 < nlocal) factor++;
if (i2 < nlocal) factor++;
if (i3 < nlocal) factor++;
}
rfactor = factor/3.0;
// 1st bond
delx1 = x[i1][0] - x[i2][0];
dely1 = x[i1][1] - x[i2][1];
delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(&delx1,&dely1,&delz1);
rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
r1 = sqrt(rsq1);
// 2nd bond
delx2 = x[i3][0] - x[i2][0];
dely2 = x[i3][1] - x[i2][1];
delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(&delx2,&dely2,&delz2);
rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
r2 = sqrt(rsq2);
// angle (cos and sin)
c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
s = sqrt(1.0 - c*c);
if (s < SMALL) s = SMALL;
s = 1.0/s;
// force & energy
dtheta = acos(c) - theta0[type];
tk = k[type] * dtheta;
if (eflag) energy += rfactor * tk*dtheta;
a = 2.0 * tk * s;
a11 = a*c / rsq1;
a12 = -a / (r1*r2);
a22 = a*c / rsq2;
vx1 = a11*delx1 + a12*delx2;
vx2 = a22*delx2 + a12*delx1;
vy1 = a11*dely1 + a12*dely2;
vy2 = a22*dely2 + a12*dely1;
vz1 = a11*delz1 + a12*delz2;
vz2 = a22*delz2 + a12*delz1;
// apply force to each of 3 atoms
if (newton_bond || i1 < nlocal) {
f[i1][0] -= vx1;
f[i1][1] -= vy1;
f[i1][2] -= vz1;
}
if (newton_bond || i2 < nlocal) {
f[i2][0] += vx1 + vx2;
f[i2][1] += vy1 + vy2;
f[i2][2] += vz1 + vz2;
}
if (newton_bond || i3 < nlocal) {
f[i3][0] -= vx2;
f[i3][1] -= vy2;
f[i3][2] -= vz2;
}
// virial contribution
if (vflag) {
virial[0] -= rfactor * (delx1*vx1 + delx2*vx2);
virial[1] -= rfactor * (dely1*vy1 + dely2*vy2);
virial[2] -= rfactor * (delz1*vz1 + delz2*vz2);
virial[3] -= rfactor * (delx1*vy1 + delx2*vy2);
virial[4] -= rfactor * (delx1*vz1 + delx2*vz2);
virial[5] -= rfactor * (dely1*vz1 + dely2*vz2);
}
}
}
/* ---------------------------------------------------------------------- */
void AngleHarmonic::allocate()
{
allocated = 1;
int n = atom->nangletypes;
k = (double *) memory->smalloc((n+1)*sizeof(double),"angle:k");
theta0 = (double *) memory->smalloc((n+1)*sizeof(double),"angle:theta0");
setflag = (int *) memory->smalloc((n+1)*sizeof(int),"angle:setflag");
for (int i = 1; i <= n; i++) setflag[i] = 0;
}
/* ----------------------------------------------------------------------
set coeffs for one or more types
------------------------------------------------------------------------- */
void AngleHarmonic::coeff(int which, int narg, char **arg)
{
if (which != 0) error->all("Invalid coeffs for this angle style");
if (narg != 3) error->all("Incorrect args for angle coefficients");
if (!allocated) allocate();
int ilo,ihi;
force->bounds(arg[0],atom->nangletypes,ilo,ihi);
double k_one = atof(arg[1]);
double theta0_one = atof(arg[2]);
// convert theta0 from degrees to radians
int count = 0;
for (int i = ilo; i <= ihi; i++) {
k[i] = k_one;
theta0[i] = theta0_one/180.0 * PI;
setflag[i] = 1;
count++;
}
if (count == 0) error->all("Incorrect args for angle coefficients");
}
/* ---------------------------------------------------------------------- */
double AngleHarmonic::equilibrium_angle(int i)
{
return theta0[i];
}
/* ----------------------------------------------------------------------
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void AngleHarmonic::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void AngleHarmonic::read_restart(FILE *fp)
{
allocate();
if (comm->me == 0) {
fread(&k[1],sizeof(double),atom->nangletypes,fp);
fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
}
MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
}
/* ---------------------------------------------------------------------- */
double AngleHarmonic::single(int type, int i1, int i2, int i3, double rfactor)
{
double **x = atom->x;
double delx1 = x[i1][0] - x[i2][0];
double dely1 = x[i1][1] - x[i2][1];
double delz1 = x[i1][2] - x[i2][2];
domain->minimum_image(&delx1,&dely1,&delz1);
double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
double delx2 = x[i3][0] - x[i2][0];
double dely2 = x[i3][1] - x[i2][1];
double delz2 = x[i3][2] - x[i2][2];
domain->minimum_image(&delx2,&dely2,&delz2);
double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
c /= r1*r2;
if (c > 1.0) c = 1.0;
if (c < -1.0) c = -1.0;
double dtheta = acos(c) - theta0[type];
double tk = k[type] * dtheta;
return (rfactor * tk*dtheta);
}
Event Timeline
Log In to Comment